Research Topics
Genomes and Genes | Pan DuSummaryAffiliation: Northwestern University Country: USA Publications
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Detail Information
Publications
lumi: a pipeline for processing Illumina microarrayPan Du
Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
Bioinformatics 24:1547-8. 2008..Availability: The lumi Bioconductor package, www.bioconductor.org..
2009 and beyond: the decade of personalised medicinePan Du
The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
Int J Comput Biol Drug Des 1:329-33. 2008....
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysisPan Du
Northwestern University Biomedical Informatics Center NUBIC, NUCATS, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
BMC Bioinformatics 11:587. 2010..Both Beta-value and M-value statistics have been used as metrics to measure methylation levels. However, there are no detailed studies of their relations and their strengths and limitations...- Gene expression and functional studies of the optic nerve head astrocyte transcriptome from normal African Americans and Caucasian Americans donorsHaixi Miao
Department of Ophthalmology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
PLoS ONE 3:e2847. 2008.... - L-methionine-induced alterations in molecular signatures in MCF-7 and LNCaP cancer cellsMaximo A Benavides
Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
J Cancer Res Clin Oncol 137:441-53. 2011..Methionine inhibits proliferation of breast and prostate cancer cells. Here, we determined the influence of L-methionine on functional molecular signatures in these cell lines... - Gene expression variation between African Americans and whites is associated with coronary artery calcification: the multiethnic study of atherosclerosisChiang Ching Huang
Department of Preventive Medicine, Northwestern University, Chicago, Illinois, USA
Physiol Genomics 43:836-43. 2011..Our data suggest a connection between immune response and vascular calcification and the result provides a potential mechanistic explanation for the lower prevalence and severity of CAC in African Americans compared with whites... - DNA methylation alterations in response to pesticide exposure in vitroXiao Zhang
Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
Environ Mol Mutagen 53:542-9. 2012..Further studies in other cell types and human samples are required, as well as determining the impact of these methylation changes on gene expression... - Visual presentation as a welcome alternative to textual presentation of gene annotation informationJairav Desai
The Biomedical Informatics Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
Adv Exp Med Biol 680:709-15. 2010..Moreover, the survey participants provided many constructive comments that will specify the development of a phase-two project (http://128.248.174.241/) to visually annotate each gene in the human genome... - Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitroXiao Zhang
Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
Environ Toxicol Pharmacol 34:959-68. 2012..2-fold, q-value=0.002), and some remain functionally unknown. Our results provided direct experimental evidence that diazinon may modify gene promoter DNA methylation levels, which may play a pathological role in cancer development... - Egr-1 induces a profibrotic injury/repair gene program associated with systemic sclerosisSwati Bhattacharyya
Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
PLoS ONE 6:e23082. 2011..These observations suggest that targeting Egr-1 expression or activity might be a novel therapeutic strategy to control fibrosis in specific SSc subsets... - Gene expression changes in retinal Müller (glial) cells exposed to elevated pressureWei Xue
Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 606111, USA
Curr Eye Res 36:754-67. 2011..To address this question, we have examined gene expression changes in Müller cells exposed to elevated pressure... - Genome-wide DNA methylation indicates silencing of tumor suppressor genes in uterine leiomyomaAntonia Navarro
Division of Reproductive Biology Research, Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
PLoS ONE 7:e33284. 2012..Epigenetic dysregulation of individual genes has been demonstrated in leiomyoma cells; however, the in vivo genome-wide distribution of such epigenetic abnormalities remains unknown... - The early growth response gene Egr2 (Alias Krox20) is a novel transcriptional target of transforming growth factor-β that is up-regulated in systemic sclerosis and mediates profibrotic responsesFeng Fang
Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
Am J Pathol 178:2077-90. 2011..Together, these findings suggest that Egr-2 plays an important nonredundant role in the pathogenesis of fibrosis. Targeting Egr-2 might represent a novel therapeutic strategy to control fibrosis... - Suppression by L-methionine of cell cycle progression in LNCaP and MCF-7 cells but not benign cellsMaximo A Benavides
Department of Pathology, University of Illinois at Chicago, College of Medicine, 840 South Wood Street, Chicago, Illinois 60612, USA
Anticancer Res 30:1881-5. 2010..Methionine inhibits proliferation of breast and prostate cancer cells. This study aimed to determine cell cycle effects of methionine and selectivity for cancer cells... - Model-based variance-stabilizing transformation for Illumina microarray dataSimon M Lin
Robert H Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, 60611, USA
Nucleic Acids Res 36:e11. 2008..The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org... - Genomics of human intracranial aneurysm wallChangbin Shi
Department of Neurological Surgery, Center for Genetic Medicine, and Robert H Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Ill 60611, USA
Stroke 40:1252-61. 2009..However, a broad view of pathologic mechanisms has not been investigated by identifying pathogenic genes and their interaction in networks. Our study aimed to analyze global gene expression patterns in the IA wall... - Activated TLR signaling in atherosclerosis among women with lower Framingham risk score: the multi-ethnic study of atherosclerosisChiang Ching Huang
Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
PLoS ONE 6:e21067. 2011.... - From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associationsPan Du
The Biomedical Informatics Center, Northwestern University, Chicago, IL 60611, USA
Bioinformatics 25:i63-8. 2009..The resultant DOLite has been used in the Functional Disease Ontology (FunDO) Web application at http://www.projects.bioinformatics.northwestern.edu/fundo... - A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarraysChia Ju Lee
Computational Biology and Bioinformatics Program, Northwestemrn University, Evanston, IL 60208, USA
Int J Comput Biol Drug Des 1:396-405. 2008..In addition to the performance improvement, the general divide-and-conquer strategy can be applied to any other normalisation algorithms without modifying the underlying implementation... - A collection of bioconductor methods to visualize gene-list annotationsGang Feng
Northwestern University Biomedical Informatics Center NUBIC, part of the Northwestern CTSA and The Robert H, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
BMC Res Notes 3:10. 2010..abstract:.. - Susceptibility to glaucoma: differential comparison of the astrocyte transcriptome from glaucomatous African American and Caucasian American donorsThomas J Lukas
Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, E Chicago Ave, Chicago, IL 60611, USA
Genome Biol 9:R111. 2008.... - Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matchingPan Du
Robert H. Lurie Comprehensive Cancer Center, Northwestern University Chicago, IL 60611, USA
Bioinformatics 22:2059-65. 2006..AVAILABILITY: The algorithm is implemented in R and will be included as an open source module in the Bioconductor project... - Expression of cyclophilin B is associated with malignant progression and regulation of genes implicated in the pathogenesis of breast cancerFeng Fang
Breast Cancer Program, Robert H Lurie Comprehensive Cancer Center and Department of Pathology, Northwestern University, Chicago, Illinois 60611, USA
Am J Pathol 174:297-308. 2009.... - Epithelial regulation of mesenchymal tissue behaviorCorrie L Gallant-Behm
Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
J Invest Dermatol 131:892-9. 2011..These results support the idea that soluble factors produced by the epithelium in response to injury may influence fibroblast behavior and regulate scar formation in vivo... - Using Free and Open-Source Bioconductor Packages to Analyze Array Comparative Genomics Hybridization (aCGH) DataSimon Lin
Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
Curr Genomics 10:60-3. 2009..We review several free and open-source packages in Bioconductor and provide example codes to run the analysis. The analysis of aCGH data provides insights of genomic abnormalities of cancers... - Modeling gene expression networks using fuzzy logicPan Du
Virtual Reality Applications Center, Iowa State University, Ames 50011-3060, USA
IEEE Trans Syst Man Cybern B Cybern 35:1351-9. 2005..Key gene regulatory relationships were evaluated using information from the gene ontology database. A new regulatory relationship concerning trehalose regulation of carbohydrate metabolism was also discovered in the extracted network...